Variant report

Variant	rs7861559
Chromosome Location	chr9:6447140-6447141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6443738..6445353-chr9:6446588..6448853,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10115362	0.82[ASN][1000 genomes]
rs10115883	0.80[ASN][1000 genomes]
rs10122116	0.80[ASN][1000 genomes]
rs10124572	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10125914	0.80[ASN][1000 genomes]
rs10733529	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739098	0.91[ASN][1000 genomes]
rs10739099	0.93[ASN][1000 genomes]
rs10739100	0.93[ASN][1000 genomes]
rs10739102	0.90[ASN][1000 genomes]
rs10758783	0.83[ASN][1000 genomes]
rs10758784	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10758785	0.89[ASN][1000 genomes]
rs10758786	0.90[ASN][1000 genomes]
rs10758787	0.90[ASN][1000 genomes]
rs10758788	0.93[ASN][1000 genomes]
rs10758789	0.93[ASN][1000 genomes]
rs10758790	0.93[ASN][1000 genomes]
rs10758791	0.89[ASN][1000 genomes]
rs10758792	0.95[ASN][1000 genomes]
rs10815428	0.82[ASN][1000 genomes]
rs10815435	0.90[ASN][1000 genomes]
rs10975579	0.85[ASN][1000 genomes]
rs10975582	0.86[ASN][1000 genomes]
rs10975583	0.90[ASN][1000 genomes]
rs10975585	0.89[ASN][1000 genomes]
rs10975595	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10975603	0.81[ASN][1000 genomes]
rs10975605	0.80[ASN][1000 genomes]
rs1156747	0.90[ASN][1000 genomes]
rs11790625	0.97[ASN][1000 genomes]
rs11791651	0.91[ASN][1000 genomes]
rs11795355	0.80[ASN][1000 genomes]
rs12346455	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347573	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12351293	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12376117	0.82[ASN][1000 genomes]
rs13283381	0.88[EUR][1000 genomes]
rs13289925	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13291472	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13292799	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13296970	0.84[EUR][1000 genomes]
rs13301146	0.84[EUR][1000 genomes]
rs13440427	0.92[ASN][1000 genomes]
rs1381035	0.93[ASN][1000 genomes]
rs1381036	0.93[ASN][1000 genomes]
rs1381037	0.92[ASN][1000 genomes]
rs16924562	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16924591	0.93[ASN][1000 genomes]
rs16924624	0.84[ASN][1000 genomes]
rs16924631	0.80[ASN][1000 genomes]
rs1824537	0.92[ASN][1000 genomes]
rs1870696	0.93[ASN][1000 genomes]
rs1903419	0.93[ASN][1000 genomes]
rs2065074	0.90[ASN][1000 genomes]
rs2065075	0.89[ASN][1000 genomes]
rs2169283	0.86[ASN][1000 genomes]
rs2169286	0.89[ASN][1000 genomes]
rs2381444	0.85[ASN][1000 genomes]
rs3739654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs380674	0.89[ASN][1000 genomes]
rs394137	0.83[ASN][1000 genomes]
rs414107	0.86[ASN][1000 genomes]
rs4380997	0.87[ASN][1000 genomes]
rs4384035	0.93[ASN][1000 genomes]
rs4463484	0.80[ASN][1000 genomes]
rs452135	0.85[ASN][1000 genomes]
rs4556138	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4740844	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4740845	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742199	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742201	0.93[ASN][1000 genomes]
rs4742202	0.93[ASN][1000 genomes]
rs4742204	0.88[ASN][1000 genomes]
rs504698	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs530722	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55960819	0.94[ASN][1000 genomes]
rs56218473	0.91[ASN][1000 genomes]
rs56396114	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56939673	0.86[ASN][1000 genomes]
rs569866	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6477086	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6477087	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67852216	0.82[ASN][1000 genomes]
rs7027302	0.94[ASN][1000 genomes]
rs7029772	0.82[EUR][1000 genomes]
rs7033940	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7034328	0.83[ASN][1000 genomes]
rs73399080	0.82[ASN][1000 genomes]
rs73401679	0.87[ASN][1000 genomes]
rs7848831	0.87[EUR][1000 genomes]
rs7852539	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7853059	0.87[ASN][1000 genomes]
rs7853834	0.87[ASN][1000 genomes]
rs7857628	0.81[ASN][1000 genomes]
rs7860427	0.82[ASN][1000 genomes]
rs7860966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865955	0.83[ASN][1000 genomes]
rs7871134	0.90[ASN][1000 genomes]
rs7873756	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7876000	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7861559	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6449000	Weak transcription	Gastric	stomach
2	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
4	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
5	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
6	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:6421400-6449400	Weak transcription	Liver	Liver
8	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
9	chr9:6422800-6449200	Weak transcription	Pancreas	Pancrea
10	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:6429600-6449200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:6431200-6449000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:6431200-6449200	Weak transcription	Adipose Nuclei	Adipose
14	chr9:6434400-6449200	Weak transcription	A549	lung
15	chr9:6434800-6447200	Weak transcription	Brain Anterior Caudate	brain
16	chr9:6435000-6460400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:6435000-6463800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:6436000-6447800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:6436600-6449200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:6437000-6447400	Weak transcription	HSMM	muscle
22	chr9:6437000-6447800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:6438000-6449000	Weak transcription	Spleen	Spleen
24	chr9:6438000-6449000	Weak transcription	HMEC	breast
25	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:6438600-6449000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:6438600-6460000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:6438800-6447400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:6438800-6447400	Weak transcription	Hela-S3	cervix
30	chr9:6438800-6449200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:6439000-6447600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:6439000-6449600	Weak transcription	NH-A	brain
33	chr9:6439400-6447800	Weak transcription	Small Intestine	intestine
34	chr9:6439600-6447200	Weak transcription	Primary T cells from cord blood	blood
35	chr9:6439600-6449200	Weak transcription	K562	blood
36	chr9:6439800-6449000	Weak transcription	Brain Substantia Nigra	brain
37	chr9:6440600-6449600	Weak transcription	NHLF	lung
38	chr9:6441400-6447200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:6441600-6448000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:6441600-6454600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:6442000-6447600	Weak transcription	GM12878-XiMat	blood
43	chr9:6442200-6455800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:6442800-6449000	Weak transcription	Left Ventricle	heart
45	chr9:6442800-6449000	Weak transcription	Ovary	ovary
46	chr9:6443000-6447200	Weak transcription	HUVEC	blood vessel
47	chr9:6443000-6447800	Weak transcription	Fetal Heart	heart
48	chr9:6443000-6461600	Weak transcription	HepG2	liver
49	chr9:6443400-6447800	Weak transcription	Brain Angular Gyrus	brain
50	chr9:6443400-6448600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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